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Sample GSM209851 Query DataSets for GSM209851
Status Public on Jan 31, 2008
Title SB90_2
Sample type RNA
 
Source name SB90-treated embryonic primary chondrocyte cultures, incubated for 24hrs.
Organism Mus musculus
Characteristics Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in α-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM β-glycerophosphate,
0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°C in a humidified 5% CO2 incubator overnight. The following morning media was removed and the bones placed in 4 ml
of 0.25% trypsin-EDTA (Invitrogen) for 15 min at 37oC. Trypsin was subsequently replaced with 1 mg/ml collagenase P (Roche) in DMEM / 10% fetal bovine serum (Invitrogen), and cells
were incubated at 37°C with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted.
Chondrocytes were resuspended in media containing 2:3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml).
Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 10 µM
SB90 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.
Biomaterial provider Mouse supplier: Charles River. Cultures were completed in Frank Beier's laboratory by Veronica Ulici and Claudine James and Lee-Anne Stanton
Treatment protocol SEE CHARACTERISTICS
Growth protocol SEE CHARACTERISTICS
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy extraction
Label SAPE
Label protocol Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/
 
Hybridization protocol LRGC specifications
Scan protocol M.A.S. 5.0-see LRGC specifications
Description AFFY551
Data processing Microarray data were pre-processed RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley. Background adjustment and quantile
normalization parameters were selected for data processing. Logarithmically transformed expression values were used to implement Gene Set Enrichment Analysis (GSEA) (Subramanian et al., 2005, PNAS).
 
Submission date Jul 11, 2007
Last update date Aug 28, 2018
Contact name Claudine James
E-mail(s) claudinegj@hotmail.com, fbeier@uwo.ca
Phone (519)661-3387
Fax (519)850-2459
Organization name University of Western Ontario
Department Physiology and Pharmacology
Lab Frank Beier/ CIHR Group in Skeletal Development and Remodeling
Street address 1151 Richmond Street, Suite 2
City London
State/province Ontario
ZIP/Postal code N6A 5C1
Country Canada
 
Platform ID GPL1261
Series (1)
GSE8488 Inhibitor Trials
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMAExpress-processed signal intensity

Data table
ID_REF VALUE
1415670_at 11.051536
1415671_at 11.241178
1415672_at 11.497983
1415673_at 9.012029
1415674_a_at 10.089373
1415675_at 9.897532
1415676_a_at 12.206686
1415677_at 9.652705
1415678_at 10.528765
1415679_at 11.341427
1415680_at 10.041501
1415681_at 9.745055
1415682_at 9.397759
1415683_at 11.304448
1415684_at 9.558366
1415685_at 8.865629
1415686_at 10.495399
1415687_a_at 11.575577
1415688_at 10.709035
1415689_s_at 8.914936

Total number of rows: 45101

Table truncated, full table size 898 Kbytes.




Supplementary file Size Download File type/resource
GSM209851.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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